Release 20
Goals and Timeline for Release #20
Timeline for Release: Goal is around the end of July or early Aug 2013
- database should be loaded and available on the beta browser by Friday Aug 2nd
Summary and Announcements
The latest release of the Plant Ontology, version #20, is available on our Plant Ontology Browser.
This full release features the addition of 48 new terms, for both the Plant Anatomical Entity (44) and Plant Structure Development Stage (4) branches. It also includes new and updated annotation data for Oryza sativa, Gossypium hirsutum and Arabidopsis thaliana.
-Includes all revisions from 1761 and on.
-For more information, please see also: Details_of_Changes_to_Release_20
The release features revision to the following sections:
Revisions to the plant anatomical entity branch:
Continue major revision of PSDS
Focus on the revisions on:
PO:0007033 : whole plant development stage
> PO:0028002 : sporophyte development stage
>> PO:0007130 : sporophyte reproductive stage [46604]: (Some still have the numbers preceding them, others don't)
>>> PO:0007047 : 3 inflorescence detectable stage [29131]
>>>PO:0007016 : 4 flowering [28057]
>>>PO:0007042 : 5 fruit formation [31009]
>>>PO:0007010 : 6 ripening [37642]
>> PO:0007134 : sporophyte vegetative stage [60370]: (Some still have the numbers preceding them, others don't)
>>>PO:0007057 : 0 seed germination stage [29568]
>>>PO:0007112 : 1 main shoot growth stage [47411]
>>>PO:0007131 : seedling development stage [26673]
PO:0009012 : plant structure development stage:
> PO:0007615 : flower development stage [48067]
>PO:0001083 : inflorescence development stage [48067]
PO:0025339 : plant organ development stage [46618]
>PO:0001050 : leaf development stage [45968]
>PO:0007520 : root development stage [25208]
PO:0025338 : collective plant structure development stage [49645]
>PO:0007615 : flower development stage [48067]
Other
- Error in the header: in current version (r1916) and line 26, the tag is misspelled. You currently have a tag called treat-xrefs-as-genus-differntia in the header. The correct spelling is treat-xrefs-as-genus-differentia (Note the additional 'e' in differentia). Judging from the SVN logs, this error has been there for more than one year. inferences may be slightly incomplete or otherwise affected. Once fixed,should check your inferences, just to be sure.
Fixed- In revision 1964
Annotation Guidelines
Comments from PJ from previous meeting (9-27-11): Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR
-This will also be helpful when applying for new grants
-it would be helpful to have a detailed guide on our wiki for collaborators
Tabled for the next release:
Continue revisions and adding new terms for wood ontology
Most terms are in the PAE branch or for GO.
Can continue to add annotations as we go along, as well.
Potato Annotations
LC has been in contact with the group who published the potato genome paper and they are interested in collaborating with us to assign ontology terms to the annotations.
From Dr. Richard Finker (Wageningen, The Netherlands):
"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."
This will go in the next release, do they have expression data- RNA Seq?
Wood Annotations
TreeGenes and Fagaceae Genomics Web
